After he was traded, Williams' career took off. While in San Diego that season, he posted an 8–8 win–loss record with a 4.97 ERA in 23 starts, but with St. Louis, Williams went 7–1 with a 2.28 ERA in 11 starts.

After the 2004 season came to a close, Williams filed for free agency and signed back with the Padres on December 9, 2004.

On November 24, 2006, the Houston Astros announced they had signed Williams to a two-year, $12.5 million contract, at the same press conference announcing the Carlos Lee signing.[3]

After a career-worst 2007 season with Houston, where he went 8–15 with a 5.27 ERA, and a poor showing during the 2008spring training, Williams was released by the Astros on March 29 and subsequently retired.

Williams used an assortment of different pitches against opposing batters. He used a cut fastball which he could throw between 89–92 mph, which was considered his best pitch overall. He relied on his curveball as his strikeout pitch, and utilized a straight change as well. Williams was also known to throw an occasional knuckleball in games.

Woody is active in the Alvin, Texas community. In 2002, he donated money to the Alvin High School athletic program to help buy new equipment. He also trained with the Alvin High baseball team before heading off to spring training.[citation needed]

He has five children. Katelyn, Sarah, Hannah, Caden, and Lillian and currently resides in Houston with them and his wife. His cousin Chase Ortiz was a defensive end for the Winnipeg Blue Bombers of the Canadian Football League. Williams began coaching varsity baseball at Fort Bend Baptist Academy in 2009, and led the team to the Texas Class 4A semifinals in both 2010 and 2011.[5]